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Crystal structure of HIV protease- metallacarborane complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NH0 PDB entry 1nh0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 277 2.0M Ammonium dihydrogen Phospate, 0.1M Tric.Cl pH 8.5, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.45 49.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.321 α = 90 b = 67.181 β = 94.99 c = 42.498 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH Flat pre-mirror, a fixed-exit sagital focusing double Silicon (111) crystal monochromator and a vertical focusing mirror. Both mirrors are Rhodium-coated. 2004-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.800 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.14 50 99.9 0.055 9.3 7.4 12431 43.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.14 2.19 99.2 0.228 3 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1nh0 2.15 28.81 12431 642 99.98 0.17864 0.17592 0.1793 0.23258 0.2391 RANDOM 38.384
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.02 0.05 -0.02 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.898 r_dihedral_angle_4_deg 18.26 r_dihedral_angle_3_deg 16.485 r_dihedral_angle_1_deg 7.555 r_scangle_it 4.13 r_scbond_it 2.674 r_angle_refined_deg 1.929 r_mcangle_it 1.513 r_mcbond_it 0.925 r_chiral_restr 0.884
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.898 r_dihedral_angle_4_deg 18.26 r_dihedral_angle_3_deg 16.485 r_dihedral_angle_1_deg 7.555 r_scangle_it 4.13 r_scbond_it 2.674 r_angle_refined_deg 1.929 r_mcangle_it 1.513 r_mcbond_it 0.925 r_chiral_restr 0.884 r_nbtor_refined 0.326 r_symmetry_vdw_refined 0.273 r_nbd_refined 0.227 r_symmetry_hbond_refined 0.215 r_xyhbond_nbd_refined 0.185 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1520 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 46
Software Software Software Name Purpose XDS data scaling SCALEPACK data scaling MOLREP phasing REFMAC refinement XDS data reduction